Re: [AMBER] limit of joining residues

From: Jio M <jiomm.yahoo.com>
Date: Sun, 14 Feb 2010 03:42:34 -0800 (PST)

Dear AMBER users and Bill Ross;




>You should send the generated script so people can get a look at it.



the script so used, is created in number of files, which are used one
by one after minimising number of joined residues as defined in one
file. It is saved finally as pdb which is used again by removing
hydrogens (to save as pdb and remove hydrogens other programe works) to
join residues defined in second file. The whole process works like as
shown below, which is one of the files which define residues to be
joined. One by one file is used, hence, to join the residues



"there" may be other ways to join same residues, but this sort of
script is used to not to get confused. This is just a small case shown
below.



e.g.



source leaprc.gaff

loadoff residues.lib

aaa = loadpdb user.pdb

bondbydistance aaa

set bbb head bbb.1.N4

set ccc head ccc.1.N1

set aaa tail aaa.2.C7

aaa = sequence {aaa bbb}

set aaa tail aaa.2.C8

aaa = sequence {aaa bbb}

set aaa tail aaa.3.C7

aaa = sequence {aaa bbb}

set aaa tail aaa.3.C8

aaa = sequence {aaa bbb}

set aaa tail aaa.4.C7

aaa = sequence {aaa bbb}

set aaa tail aaa.4.C8

aaa = sequence {aaa bbb}

set aaa tail aaa.5.C7

aaa = sequence {aaa bbb}

set aaa tail aaa.5.C8

aaa = sequence {aaa bbb}

set aaa tail aaa.6.C7

aaa = sequence {aaa bbb}

set aaa tail aaa.6.C8

aaa = sequence {aaa bbb}

set aaa tail aaa.7.C7

aaa = sequence {aaa bbb}

set aaa tail aaa.7.C8

aaa = sequence {aaa bbb}

set aaa tail aaa.8.C7

aaa = sequence {aaa bbb}

set aaa tail aaa.8.C8

aaa = sequence {aaa bbb}

set aaa tail aaa.9.C7

aaa = sequence {aaa bbb}

set aaa tail aaa.9.C8

aaa = sequence {aaa bbb}

set aaa tail aaa.10.C7

aaa = sequence {aaa bbb}

set aaa tail aaa.10.C8

aaa = sequence {aaa bbb}

set aaa tail aaa.11.C7

aaa = sequence {aaa bbb}

set aaa tail aaa.11.C8

aaa = sequence {aaa bbb}

set aaa tail aaa.12.C7

aaa = sequence {aaa bbb}

set aaa tail aaa.12.C8

aaa = sequence {aaa bbb}

set aaa tail aaa.13.C7

aaa = sequence {aaa bbb}

set aaa tail aaa.13.C8

aaa = sequence {aaa bbb}

saveamberparm aaa xyz.prmtop xyz.inpcrd

quit



thanks and regards;



JIomm

> Script (that is how to join residues) is written by some programme



You should send the generated script so people can get a look at it.



Bill


      
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Received on Sun Feb 14 2010 - 04:00:02 PST
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